Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using PRISM

Nurcan Tuncbag, Attila Gursoy*, Ruth Nussinov, Ozlem Keskin

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

239 Scopus citations

Abstract

Prediction of protein-protein interactions at the structural level on the proteome scale is important because it allows prediction of protein function, helps drug discovery and takes steps toward genome-wide structural systems biology. We provide a protocol (termed PRISM, protein interactions by structural matching) for large-scale prediction of protein-protein interactions and assembly of protein complex structures. The method consists of two components: rigid-body structural comparisons of target proteins to known template protein-protein interfaces and flexible refinement using a docking energy function. The PRISM rationale follows our observation that globally different protein structures can interact via similar architectural motifs. PRISM predicts binding residues by using structural similarity and evolutionary conservation of putative binding residue 'hot spots'. Ultimately, PRISM could help to construct cellular pathways and functional, proteome-scale annotation. PRISM is implemented in Python and runs in a UNIX environment. The program accepts Protein Data Bank-formatted protein structures and is available at http://prism.ccbb.ku.edu.tr/prism-protocol/.

Original languageEnglish
Pages (from-to)1341-1354
Number of pages14
JournalNature Protocols
Volume6
Issue number9
DOIs
StatePublished - Sep 2011

Funding

FundersFunder number
TUBA
Türkiye Bilimler Akademisi
Not added109T343
National Cancer InstituteZIABC010441, ZIABC010440
National Institutes of HealthHHSN261200800001E
TUBITAK109E207

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